def addNewOs(new_res, psi, **kw):
new_N = new_res.atomsMap['N'][0]
new_CA = new_res.atomsMap['CA'][0]
new_C = new_res.atomsMap['C'][0]
new_OXT = addDihedralAtom('OXT',
chimera.Element(8),
new_C,
new_CA,
new_N,
DIST_C_O,
114,
psi,
residue=new_res)
new_OXT.drawMode = kw['atomDrawMode']
new_OXT.bfactor = kw['bFactor']
addBond(new_OXT, new_C, drawMode=kw['bondDrawMode'])
avail_bond_pos = bondPositions(bondee=new_C.coord(),
geom=chimera.Atom.Planar,
bondLen=DIST_C_O,
bonded=[a.coord() for a in new_C.neighbors])
use_point = avail_bond_pos[0]
new_O = addAtom('O', chimera.Element(8), new_res, use_point)
new_O.drawMode = kw['atomDrawMode']
new_O.bfactor = kw['bFactor']
addBond(new_O, new_C, drawMode=kw['bondDrawMode'])
return new_O, new_OXT
def _processMolecules(self, topFile):
molInfo = {
'SOL': [
# atoms
[('OW', chimera.Element('O'), 1),
('HW1', chimera.Element('H'), 1),
('HW2', chimera.Element('H'), 1)],
# atom map
{
0: 0,
1: 1,
2: 2
},
# res names
['SOL'],
# res map
{
1: 0
},
# bonds
[[0, 1], [0, 2]]
]
}
molInfo.update(self.molInfo)
curRes = None
line = self._readLine(topFile)
while line:
molType, num = line.split()
num = int(num)
try:
atoms, atomMap, resNames, resMap, bonds = \
molInfo[molType]
except KeyError:
raise ValueError("Unknown molecule type: %s" % molType)
for i in range(num):
resBase = len(self.resNames)
atomBase = len(self.atomNames)
self.resNames.extend(resNames)
for atomName, element, resLookup in atoms:
self.atomNames.append(atomName)
resIndex = resBase + resMap[resLookup]
if resIndex != curRes:
self.resIndices.append(len(self.atomNames))
curRes = resIndex
self.elements.append(element)
for a1, a2 in bonds:
i1, i2 = atomMap[a1], atomMap[a2]
self.bonds.append((atomBase + i1, atomBase + i2))
line = self._readLine(topFile)
return False
def _methylate(na, n, atomNames):
added = []
aname = _getAName("C", atomNames)
from chimera.molEdit import addAtom
nn = addAtom(aname, chimera.Element('C'), na.residue, n.coord())
added.append(nn)
na.molecule.newBond(na, nn)
from chimera.bondGeom import bondPositions
for pos in bondPositions(nn.coord(), 4, 1.1, [na.coord()]):
hname = _getAName("H", atomNames)
nh = addAtom(hname, chimera.Element('H'), na.residue, pos)
added.append(nh)
na.molecule.newBond(nn, nh)
return added
def _phosphorylate(mols, status, deletes):
replyobj.info("Deleting 5' phosphates from: %s\n" %
", ".join([str(r) for r in deletes]))
from chimera.molEdit import addAtom
for r in deletes:
r.amberName += "5"
for p in r.atomsMap['P']:
o = None
for nb in p.neighbors:
for nnb in nb.neighbors:
if nnb == p:
continue
if nnb.element.number > 1:
o = nb
continue
r.molecule.deleteAtom(nnb)
if nb != o:
r.molecule.deleteAtom(nb)
v = p.coord() - o.coord()
sn = getattr(p, "serialNumber", None)
r.molecule.deleteAtom(p)
v.length = 0.96
addAtom("H5T",
chimera.Element('H'),
r,
o.coord() + v,
serialNumber=sn,
bondedTo=o)
def add_dummy_atom(self,
where,
name='dum',
element=None,
residue=None,
bonded_to=None,
serial=None):
"""
Adds a placeholder atom at the coordinates specified by `where`
Parameters
----------
where : chimera.Atom or 3-tuple of float
Coordinates of target location. A chimera.Atom can be supplied,
in which case its coordinates will be used (via `.coord()`)
name : str, optional
Name for the new atom
element : chimera.Element, optional
Element of the new atom
residue : chimera.Residue, optional
Residue that will incorporate the new atom
bonded_to : chimera.Atom, optional
Atom that will form a bond with new atom
serial : int
Serial number that will be assigned to atom
"""
if isinstance(where, chimera.Atom):
element = where.element if not element else element
where = where.coord()
else:
element = chimera.Element('C')
residue = self.mol.residues[-1] if not residue else residue
return addAtom(name, element, residue, where, serial, bonded_to)
def addNewCA(last_bbone_ats, new_res, **kw):
last_CA = last_bbone_ats['CA']
last_C = last_bbone_ats['C']
last_O = last_bbone_ats['O']
new_N = new_res.atomsMap['N'][0]
## add the CA atom (not dihedral!)
## first, find the location for the new CA atom
new_CA_bond_pos = bondPositions(
bondee=new_N.coord(),
geom=chimera.Atom.Planar,
bondLen=DIST_CA_N,
bonded=[a.coord() for a in new_N.neighbors],
coPlanar=[last_CA.coord(), last_O.coord()])
shortest_point = getShortestPoint(last_O.coord(), new_CA_bond_pos)
new_CA = addAtom('CA', chimera.Element(6), new_res, shortest_point)
new_CA.drawMode = kw['atomDrawMode']
new_CA.bfactor = kw['bFactor']
addBond(new_N, new_CA, drawMode=kw['bondDrawMode'])
return new_CA
def computeElements(self):
self.elements = []
for i, atom_type in enumerate(self.prmtop['AtomSym']):
try:
elementName = atom_type_to_elements[atom_type.upper()]
except KeyError:
# use mass
from Trajectory import determineElementFromMass
el = determineElementFromMass(self.prmtop['Masses'][i])
else:
el = chimera.Element(elements.name.index(elementName))
self.elements.append(el)
def patch_mol2_reader(*args, **kwargs):
"""
Force UCSF Chimera to read UFF atom types in Mol2
"""
def parse_uff(atom_line):
atom_type = getattr(atom_line, 'mol2type',
None) or atom_line.split().fields[5]
matches = re.search(r'([A-Za-z]{1,3})[^A-Za-z\s]{0,6}', atom_type)
element = matches.group(0).title() if matches else atom_type
return element
molecules = chimera._openMol2Model_original(*args, **kwargs)
for molecule in molecules:
for atom in molecule.atoms:
atom.element = chimera.Element(parse_uff(atom))
def normalizeMSE(r):
S = chimera.Element("S")
from BuildStructure import setBondLength
for a in r.atoms:
if a.element.name != "Se":
continue
a.element = S
a.name = "SD"
a.idatmType = "S3"
for n, b in a.bondsMap.items():
if n.name == "CE":
setBondLength(b, 1.78)
elif n.name == "CG":
setBondLength(b, 1.81)
r.type = "MET"
replyobj.info("MSE residue %s changed to MET\n" % str(r))
def completeTerminalCarboxylate(cter):
from chimera.bondGeom import bondPositions
from chimera.molEdit import addAtom
if "OXT" in cter.atomsMap:
return
try:
cs = cter.atomsMap["C"]
except KeyError:
return
for c in cs: # alt locs are possible
if len(c.primaryBonds()) != 2:
return
loc = bondPositions(c.coord(), 3, 1.229,
[n.coord() for n in c.primaryNeighbors()])[0]
oxt = addAtom("OXT", chimera.Element("O"), cter, loc, bondedTo=c)
replyobj.info("Missing OXT added to C-terminal residue %s\n" % str(cter))
class FakeHydrogen: def __init__(self, atm): self.bonded = atm element = chimera.Element(1) def primaryNeighbors(self): return [self.bonded] def oslIdent(self): return 'FakeHydrogen' idatmType = 'HC' def xformCoord(self): primary = self.primaryNeighbors()[0] pos = bondPositions(primary.xformCoord(), 4, 1.0, bonds) class FakeCoord: pass crd = FakeCoord() crd = pos[0] return crd
def convert_gaussian_molecule_to_chimera(path_or_parser):
if isinstance(path_or_parser, basestring):
parsed = Gaussian(path_or_parser).parse()
else:
parsed = path_or_parser
elements = parsed.atomnos
coords = parsed.atomcoords[-1]
m = chimera.Molecule()
r = m.newResidue("UNK", " ", 1, " ")
for i, (element, xyz) in enumerate(zip(elements, coords)):
element = chimera.Element(element)
a = m.newAtom('{}{}'.format(element, i), element)
r.addAtom(a)
a.setCoord(chimera.Point(*xyz))
a.serialNumber = i
chimera.connectMolecule(m)
return m
def addNewN(last_bbone_ats, new_res, **kw):
## add the N atom of new residue's backbone to the last residue
last_C = last_bbone_ats['C']
new_N_bond_pos = bondPositions(
bondee=last_C.coord(),
geom=chimera.Atom.Planar,
bondLen=DIST_N_C,
bonded=[a.coord() for a in last_C.neighbors])
use_point = new_N_bond_pos[0]
new_N = addAtom('N', chimera.Element(7), new_res, use_point)
new_N.drawMode = kw['atomDrawMode']
new_N.bfactor = kw['bFactor']
addBond(last_C, new_N, drawMode=kw['bondDrawMode'])
return new_N
def _mutateSugarSe(r):
for a in r.atoms:
if a.name == "CA'":
for nb in a.neighbors:
if nb.element.number == 1:
r.molecule.deleteAtom(nb)
r.molecule.deleteAtom(a)
break
O = chimera.Element("O")
from BuildStructure import setBondLength
for a in r.atoms:
if a.element.name != "Se":
continue
a.element = O
a.name = "O2'"
a.idatmType = "O3"
for n, b in a.bondsMap.items():
if n.name == "C2'":
setBondLength(b, 1.43)
def reposLastO(last_res, last_bbone_ats, atom_drawMode, bond_drawMode):
## reposition the last residue's 'O' atom
last_O = getBboneAtom(last_res, 'O')
last_res.molecule.deleteAtom(last_O)
last_C = last_bbone_ats['C']
last_CA = last_bbone_ats['CA']
old_O_bond_pos = bondPositions(
bondee=last_C.coord(),
geom=chimera.Atom.Planar,
bondLen=1.229,
bonded=[a.coord() for a in last_C.neighbors])
## should only be one spot left
old_O_bond_pos = old_O_bond_pos[0]
new_O = addAtom('O', chimera.Element(8), last_res, old_O_bond_pos)
new_O.drawMode = atom_drawMode
addBond(new_O, last_C, drawMode=bond_drawMode)
return new_O
def addNewC(last_bbone_ats, new_res, phi, **kw):
last_C = last_bbone_ats['C']
new_CA = new_res.atomsMap['CA'][0]
new_N = new_res.atomsMap['N'][0]
new_C = addDihedralAtom('C',
chimera.Element(6),
new_CA,
new_N,
last_C,
DIST_C_CA,
109.5,
phi,
residue=new_res)
new_C.drawMode = kw['atomDrawMode']
new_C.bfactor = kw['bFactor']
addBond(new_CA, new_C, drawMode=kw['bondDrawMode'])
return new_C
def restoreMolecules(molInfo, resInfo, atomInfo, bondInfo, crdInfo):
from SimpleSession import registerAttribute
items = []
sm = globals.sessionMap
res2mol = []
atom2mol = []
for ids, name, cid, display, lineWidth, pointSize, stickScale, \
pdbHeaders, surfaceOpacity, ballScale, vdwDensity, autochain, \
ribbonHidesMainchain, riCID, aromaticCID, aromaticDisplay, \
aromaticLineType, aromaticMode, hidden in zip(
expandSummary(molInfo['ids']),
expandSummary(molInfo['name']),
expandSummary(molInfo['color']),
expandSummary(molInfo['display']),
expandSummary(molInfo['lineWidth']),
expandSummary(molInfo['pointSize']),
expandSummary(molInfo['stickScale']),
molInfo['pdbHeaders'],
expandSummary(molInfo['surfaceOpacity']),
expandSummary(molInfo['ballScale']),
expandSummary(molInfo['vdwDensity']),
expandSummary(molInfo['autochain']),
expandSummary(molInfo['ribbonHidesMainchain']),
expandSummary(molInfo['ribbonInsideColor']),
expandSummary(molInfo['aromaticColor']),
expandSummary(molInfo['aromaticDisplay']),
expandSummary(molInfo['aromaticLineType']),
expandSummary(molInfo['aromaticMode']),
expandSummary(molInfo['hidden'])
):
m = chimera.Molecule()
sm[len(items)] = m
items.append(m)
m.name = name
from SimpleSession import modelMap, modelOffset
chimera.openModels.add([m],
baseId=ids[0] + modelOffset,
subid=ids[1],
hidden=hidden)
modelMap.setdefault(ids, []).append(m)
m.color = getColor(cid)
m.display = display
m.lineWidth = lineWidth
m.pointSize = pointSize
m.stickScale = stickScale
m.setAllPDBHeaders(pdbHeaders)
m.surfaceOpacity = surfaceOpacity
m.ballScale = ballScale
m.vdwDensity = vdwDensity
m.autochain = autochain
m.ribbonHidesMainchain = ribbonHidesMainchain
m.ribbonInsideColor = getColor(riCID)
m.aromaticColor = getColor(aromaticCID)
m.aromaticDisplay = aromaticDisplay
m.aromaticLineType = aromaticLineType
m.aromaticMode = aromaticMode
if molInfo['optional']:
for attrName, info in molInfo['optional'].items():
hashable, sv = info
registerAttribute(chimera.Molecule, attrName, hashable=hashable)
vals = expandSummary(sv, hashable=hashable)
for m, val in zip(items, vals):
if val is not None:
setattr(m, attrName, val)
resStart = len(items)
for mid, name, chain, pos, insert, rcid, lcid, ss, ssId, ribbonDrawMode, \
ribbonDisplay, label, labelOffset, isHet, fillDisplay, fillMode in zip(
expandSummary(resInfo['molecule']),
expandSummary(resInfo['name']),
expandSummary(resInfo['chain']),
expandSequentialSummary(resInfo['position']),
expandSummary(resInfo['insert']),
expandSummary(resInfo['ribbonColor']),
expandSummary(resInfo['labelColor']),
expandSummary(resInfo['ss']),
expandSummary(resInfo['ssId']),
expandSummary(resInfo['ribbonDrawMode']),
expandSummary(resInfo['ribbonDisplay']),
expandSummary(resInfo['label']),
expandSummary(resInfo['labelOffset']),
expandSummary(resInfo['isHet']),
expandSummary(resInfo['fillDisplay']),
expandSummary(resInfo['fillMode']),
):
m = idLookup(mid)
r = m.newResidue(name, chain, pos, insert)
sm[len(items)] = r
items.append(r)
r.ribbonColor = getColor(rcid)
r.labelColor = getColor(lcid)
r.isHelix, r.isStrand, r.isTurn = ss
r.ssId = ssId
r.ribbonDrawMode = ribbonDrawMode
r.ribbonDisplay = ribbonDisplay
r.label = label
if labelOffset is not None:
r.labelOffset = labelOffset
r.isHet = isHet
r.fillDisplay = fillDisplay
r.fillMode = fillMode
if resInfo['optional']:
residues = items[resStart:]
for attrName, info in resInfo['optional'].items():
hashable, sv = info
registerAttribute(chimera.Residue, attrName, hashable=hashable)
vals = expandSummary(sv, hashable=hashable)
for r, val in zip(residues, vals):
if val is not None:
setattr(r, attrName, val)
atomStart = len(items)
for rid, name, element, cid, vcid, lcid, scid, drawMode, display, \
label, labelOffet, surfaceDisplay, surfaceCategory, surfaceOpacity, \
radius, vdw, idatmType, altLoc in zip(
expandSummary(atomInfo['residue']),
expandSummary(atomInfo['name']),
expandSummary(atomInfo['element']),
expandSummary(atomInfo['color']),
expandSummary(atomInfo['vdwColor']),
expandSummary(atomInfo['labelColor']),
expandSummary(atomInfo['surfaceColor']),
expandSummary(atomInfo['drawMode']),
expandSummary(atomInfo['display']),
expandSummary(atomInfo['label']),
expandSummary(atomInfo['labelOffset']),
expandSummary(atomInfo['surfaceDisplay']),
expandSummary(atomInfo['surfaceCategory']),
expandSummary(atomInfo['surfaceOpacity']),
expandSummary(atomInfo['radius']),
expandSummary(atomInfo['vdw']),
expandSummary(atomInfo['idatmType']),
expandSummary(atomInfo['altLoc'])
):
r = idLookup(rid)
a = r.molecule.newAtom(name, chimera.Element(element))
sm[len(items)] = a
items.append(a)
r.addAtom(a)
a.color = getColor(cid)
a.vdwColor = getColor(vcid)
a.labelColor = getColor(lcid)
a.surfaceColor = getColor(scid)
a.drawMode = drawMode
a.display = display
a.label = label
if labelOffset is not None:
a.labelOffset = labelOffset
a.surfaceDisplay = surfaceDisplay
a.surfaceCategory = surfaceCategory
a.surfaceOpacity = surfaceOpacity
a.radius = radius
a.vdw = vdw
if idatmType:
a.idatmType = idatmType
a.altLoc = altLoc
if atomInfo['optional']:
atoms = items[atomStart:]
for attrName, info in atomInfo['optional'].items():
hashable, sv = info
registerAttribute(chimera.Atom, attrName, hashable=hashable)
vals = expandSummary(sv, hashable=hashable)
for a, val in zip(atoms, vals):
if val is not None:
setattr(a, attrName, val)
bondStart = len(items)
for atoms, drawMode, display, label, labelOffset, radius in zip(
bondInfo['atoms'], expandSummary(bondInfo['drawMode']),
expandSummary(bondInfo['display']),
expandSummary(bondInfo['label']),
expandSummary(bondInfo['labelOffset']),
expandSummary(bondInfo['radius'])):
a1, a2 = [idLookup(a) for a in atoms]
b = a1.molecule.newBond(a1, a2)
sm[len(items)] = b
items.append(b)
b.drawMode = drawMode
b.display = display
b.label = label
if labelOffset is not None:
b.labelOffset = labelOffset
b.radius = radius
if bondInfo.get('optional', {}):
bonds = items[bondStart:]
for attrName, info in bondInfo['optional'].items():
hashable, sv = info
registerAttribute(chimera.Bond, attrName, hashable=hashable)
vals = expandSummary(sv, hashable=hashable)
for b, val in zip(bonds, vals):
if val is not None:
setattr(b, attrName, val)
from chimera import Point
for mid, crdSets in crdInfo.items():
m = idLookup(mid)
active = crdSets.pop('active')
for key, crds in crdSets.items():
coordSet = m.newCoordSet(key, len(crds))
for aid, crdString in crds:
idLookup(aid).setCoord(
Point(*tuple([float(c) for c in crdString.split()])),
coordSet)
if key == active:
m.activeCoordSet = coordSet
if test == "model" and a.molecule != nb.molecule:
continue
clash = a.radius + nb.radius - a.xformCoord().distance(
nb.xformCoord())
if hbondAllowance:
if (_donor(a) and _acceptor(nb)) or (_donor(nb)
and _acceptor(a)):
clash -= hbondAllowance
if clash < clashThreshold:
continue
clashes.setdefault(a, {})[nb] = clash
clashes.setdefault(nb, {})[a] = clash
return clashes
hyd = chimera.Element(1)
negative = set([chimera.Element(sym) for sym in ["N", "O", "S"]])
from chimera.idatm import typeInfo
def _donor(a):
if a.element == hyd:
if a.neighbors and a.neighbors[0].element in negative:
return True
elif a.element in negative:
try:
if len(a.bonds) < typeInfo[a.idatmType].substituents:
# implicit hydrogen
return True
except KeyError:
pass
def ReadMol ( fpath, log=False ) :
from random import random
cif, loops = ReadCif ( fpath, log )
# descriptions by chain id:
descrByEntityId = GetEntityDescr ( cif, loops )
try :
atoms = loops['_atom_site']['data']
print " - %d atom records" % len(atoms)
except :
print " - no atoms in cif?"
return None
labels = loops['_atom_site']['labels']
if 0 :
print "Labels:"
for l in labels :
print " : ", l
import time
start = time.time()
rmap = {}
nmol = chimera.Molecule()
from os import path
#nmol.name = path.splitext ( path.split (fpath)[1] )[0]
nmol.name = path.split (fpath) [1]
nmol.openedAs = [ fpath, [] ]
nmol.cif = cif
nmol.cifLoops = loops
nmol.chainColors = {}
nmol.chainDescr = {}
numQ = 0
first = True
for at in atoms :
mp = at['asMap']
if log and first :
#for label, val in mp.iteritems () :
for li, label in enumerate ( labels ) :
print " %d : %s : %s" % (li+1, label, mp[label])
first = False
atType = mp['type_symbol']
atName = mp['label_atom_id']
rtype = mp['label_comp_id']
chainId = mp['label_asym_id']
chainEId = mp['label_entity_id']
px = mp['Cartn_x']
py = mp['Cartn_y']
pz = mp['Cartn_z']
occ = mp['occupancy']
bfactor = mp['B_iso_or_equiv']
altLoc = mp['label_alt_id']
if altLoc == "." : altLoc = ''
if chainEId in descrByEntityId :
nmol.chainDescr [chainId] = descrByEntityId [chainEId]
resId = ResId ( mp )
if resId == None :
continue
ris = "%s%d" % (chainId, resId)
res = None
if not ris in rmap :
res = nmol.newResidue ( rtype, chimera.MolResId(chainId, resId) )
rmap[ris] = res
else :
res = rmap[ris]
clr = None
if not chainId in nmol.chainColors :
clr = chimera.MaterialColor ( random(), random(), random(), 1.0 )
nmol.chainColors[chainId] = clr
if 0 and log :
print " - chain %s" % chainId
else :
clr = nmol.chainColors [chainId]
nat = nmol.newAtom ( atName, chimera.Element(atType) )
drawRib = rtype in protein3to1 or rtype in nucleic3to1
#aMap[at] = nat
res.addAtom( nat )
nat.setCoord ( chimera.Point( float(px), float(py), float(pz) ) )
nat.altLoc = altLoc
nat.occupancy = float(occ)
nat.bfactor = float(bfactor)
if 'Q-score' in mp :
try :
Q = float ( mp['Q-score'] )
nat.Q = Q
numQ += 1
except :
#print " - q score is", mp['Q-score']
pass
end = time.time()
print " - created %d atoms, %.1fs, %d q-scores" % ( len(nmol.atoms), end-start, numQ )
return nmol
def append_node(molecule, list, residue):
at = molecule.newAtom("Tunnel", chimera.Element("Tunn"))
at.setCoord(chimera.Coord(list[0], list[1], list[2]))
at.radius = list[3]
residue.addAtom(at)
def restoreMolecules(molInfo, resInfo, atomInfo, bondInfo, crdInfo):
items = []
sm = globals.sessionMap
res2mol = []
atom2mol = []
openModelsArgs = {}
for ids, name, cid, display, lineWidth, pointSize, stickScale, \
pdbHeaders, surfaceOpacity, ballScale, vdwDensity, autochain, \
ribbonHidesMainchain in zip(
expandSummary(molInfo['ids']),
expandSummary(molInfo['name']),
expandSummary(molInfo['color']),
expandSummary(molInfo['display']),
expandSummary(molInfo['lineWidth']),
expandSummary(molInfo['pointSize']),
expandSummary(molInfo['stickScale']),
molInfo['pdbHeaders'],
expandSummary(molInfo['surfaceOpacity']),
expandSummary(molInfo['ballScale']),
expandSummary(molInfo['vdwDensity']),
expandSummary(molInfo['autochain']),
expandSummary(molInfo['ribbonHidesMainchain'])
):
m = chimera.Molecule()
sm[len(items)] = m
items.append(m)
m.name = name
from SimpleSession import modelMap, modelOffset
chimera.openModels.add([m], baseId=ids[0] + modelOffset, subid=ids[1])
modelMap.setdefault(ids, []).append(m)
m.color = getColor(cid)
m.display = display
m.lineWidth = lineWidth
m.pointSize = pointSize
m.stickScale = stickScale
m.setAllPDBHeaders(pdbHeaders)
m.surfaceOpacity = surfaceOpacity
m.ballScale = ballScale
m.vdwDensity = vdwDensity
m.autochain = autochain
m.ribbonHidesMainchain = ribbonHidesMainchain
for mid, name, chain, pos, insert, rcid, lcid, ss, ribbonDrawMode, \
ribbonDisplay, label in zip(
expandSummary(resInfo['molecule']),
expandSummary(resInfo['name']),
expandSummary(resInfo['chain']),
resInfo['position'],
expandSummary(resInfo['insert']),
expandSummary(resInfo['ribbonColor']),
expandSummary(resInfo['labelColor']),
expandSummary(resInfo['ss']),
expandSummary(resInfo['ribbonDrawMode']),
expandSummary(resInfo['ribbonDisplay']),
expandSummary(resInfo['label'])
):
m = idLookup(mid)
r = m.newResidue(name, chain, pos, insert)
sm[len(items)] = r
items.append(r)
r.ribbonColor = getColor(rcid)
r.labelColor = getColor(lcid)
r.isHelix, r.isStrand, r.isTurn = ss
r.ribbonDrawMode = ribbonDrawMode
r.ribbonDisplay = ribbonDisplay
r.label = label
for rid, name, element, cid, vcid, lcid, scid, drawMode, display, \
label, surfaceDisplay, surfaceCategory, surfaceOpacity, radius, vdw, \
bfactor, occupancy, charge, idatmType in zip(
expandSummary(atomInfo['residue']),
expandSummary(atomInfo['name']),
expandSummary(atomInfo['element']),
expandSummary(atomInfo['color']),
expandSummary(atomInfo['vdwColor']),
expandSummary(atomInfo['labelColor']),
expandSummary(atomInfo['surfaceColor']),
expandSummary(atomInfo['drawMode']),
expandSummary(atomInfo['display']),
expandSummary(atomInfo['label']),
expandSummary(atomInfo['surfaceDisplay']),
expandSummary(atomInfo['surfaceCategory']),
expandSummary(atomInfo['surfaceOpacity']),
expandSummary(atomInfo['radius']),
expandSummary(atomInfo['vdw']),
expandSummary(atomInfo['bfactor']),
expandSummary(atomInfo['occupancy']),
expandSummary(atomInfo['charge']),
expandSummary(atomInfo['idatmType'])
):
r = idLookup(rid)
a = r.molecule.newAtom(name, chimera.Element(element))
sm[len(items)] = a
items.append(a)
r.addAtom(a)
a.color = getColor(cid)
a.vdwColor = getColor(vcid)
a.labelColor = getColor(lcid)
a.surfaceColor = getColor(scid)
a.drawMode = drawMode
a.display = display
a.label = label
a.surfaceDisplay = surfaceDisplay
a.surfaceCategory = surfaceCategory
a.surfaceOpacity = surfaceOpacity
a.radius = radius
a.vdw = vdw
if bfactor is not None:
a.bfactor = bfactor
if occupancy is not None:
a.occupancy = occupancy
if charge is not None:
a.charge = charge
if idatmType:
a.idatmType = idatmType
for atoms, drawMode, display in zip(bondInfo['atoms'],
expandSummary(bondInfo['drawMode']),
expandSummary(bondInfo['display'])):
a1, a2 = [idLookup(a) for a in atoms]
b = a1.molecule.newBond(a1, a2)
sm[len(items)] = b
items.append(b)
b.drawMode = drawMode
b.display = display
from chimera import Point
for mid, crdSets in crdInfo.items():
m = idLookup(mid)
active = crdSets.pop('active')
for key, crds in crdSets.items():
coordSet = m.newCoordSet(key, len(crds))
for aid, crdString in crds:
idLookup(aid).setCoord(
Point(*tuple([float(c) for c in crdString.split()])),
coordSet)
if key == active:
m.activeCoordSet = coordSet
